应用贝叶斯理论推断DNA分子标记基因型

引入贝叶斯理论用以从DNA分子标记的表现型（电泳谱带）推断其基因型（DNA来源）。结果表明,根据标记座位独立贫富而确定的遗传信息不完全标记的基因型概率,与根据令近的遗传信息完全标记的基因型和有关重组率算得的相应贝叶斯概率,通常都有很大的差异,所以在进行数量性状基因定位和标记辅助选择等工作之前,应当计算每一个体基因组上所有遗传信息不完全座位的有关基因型的贝叶斯概率。文中列出计算未知基因型的贝叶期概率的详细过程,也讨论了贝叶斯概率的若干推广应用。     

DNA分子标记信息不完全的统计处理

显性分子标记提供的有关该标记基因型的遗传信息是不完全的 ,缺失标记则丧失了它本来可能提供的遗传信息 .根据遗传学和统计学的一些基本原理 ,导出了一种通用算法 ,可以在F₂ 代群体中系统地恢复基因组上所有显性和缺失标记的基因型信息 ,从而增进构建数量性状基因图和标记辅助选择等工作的效率和精度 .这一方法也可方便地推广应用于一个标记具有 3种基因型的各类群体 ,例如由F₂ 自交衍生的高世代群体和随交群体等     

微卫星标记对牙鲆有丝分裂雌核发育家系的亲子鉴定

利用18个微卫星标记,对6个家系的26尾有丝分裂雌核发育牙鲆进行亲子鉴定,PCR扩增产物经8%非变性聚丙烯酰胺凝胶电泳检测,结果表明:1个座位在母本中表现为相同的基因型,视为单态座位,其他17个座位为多态;多态座位在亲子鉴定中的累计排除概率和累计个体识别概率分别为0.9985、0.9999;根据被测个体在17个微卫星座位的基因型,最后确认26尾子代的母本,其中7尾子代在某些座位表现出与其母本不完全匹配的基因型。利用微卫星标记可确定雌核发育后代的亲子关系,从而构建牙鲆雌核发育家系系谱,对牙鲆雌核发育的深入研究具有重要意义。     

分子标记在作物育种中的应用

近20年来发展了多种分子标记,使作物育种学家有可能直接根据基因型而不只是表现型进行选择,在作物育种的各个方面具有重要的利用价值。本文简要综述了分子标记在作物育种方面的有关应用。主要内容有：（1）分子图谱构建与基因定位;（2）DNA指纹库的建立;（3）标记辅助选择;（4）F1杂种优势分析;（5）基于图谱克隆基因。     

微卫星标记对牙鲆有丝分裂雌核发育家系的亲子鉴定

利用18个微卫星标记,对6个家系的26尾有丝分裂雌核发育牙鲆进行亲子鉴定,PCR扩增产物经8％非变性聚丙烯酰胺凝胶电泳检测,结果表明：1个座位在母本中表现为相同的基因型,视为单态座位,其他17个座位为多态;多态座位在亲子鉴定中的累计排除概率和累计个体识别概率分别为0.9985、0.9999;根据被测个体在17个微卫星座位的基因型,最后确认26尾子代的母本,其中7尾子代在某些座位表现出与其母本不完全匹配的基因型。利用微卫星标记可确定雌核发育后代的亲子关系,从而构建牙鲆雌核发育家系系谱,对牙鲆雌核发育的深入研究具有重要意义。     

DNA分子标记在实验动物遗传分析中的应用

DNA分子标记技术很多,基本都是建立在RFLP、PCR和重复顺序的基础上的。本文重点介绍了限制性片段长度多态性（RFLP）标记、随机扩增多态性DNA（RAPD）标记、微卫星DNA（STR）标记、DNA指纹（DFP）标记、扩增片段长度多态性（AFLP）标记等几种重要的DNA分子标记技术的定义、结构、分布、组成、保守性、优点及丰富的多态性等。并重点介绍了微卫星DNA（STR）标记在分子遗传监测、遗传多样性分析和遗传血缘关系及个体识别等领域的应用。     

回交育种中供体基本组成分的分布及其应用

推导了回交群体中供体基因组成分的条件概率分布,并用平均数预测各个体的供体染色体片段的大小。预测的精度则用有关方差的公式,以供体的实际片断大小（y）与根据标记基因型预测的供体片断大小（y^p)的相关表示,并表达为标记密度的函数。结果表明：虽然在标记密度中等（例如40cM／标记）时即能获得y和y^p的高度相关,但对一个在群体,仍必须通过高密度的标记图（例如10－20cM／标记）才可能鉴别出其中的最佳个体。因此,为了在标记辅助回交育种中充分利用标记信息,应当分步骤鉴定标记基因型和选择具体。这就是：先根据少数标记对所有个体作初步选择,再根据较多标记对少数个体作精细选择。这样,在基因渐渗实验中,就可以既提高对大群体的选择强度又只要鉴定有限数目的标记基因型。这是一种非常有效的方法。     

高中生物学“DNA分子复制”教学中的2点误区

误区1：DNA分子复制时不需要DNA连接酶。 例：下面哪种酶在遗传信息的传递和表达过程中不起作用（ ）。 A．DNA连接酶 B．DNA聚合酶 C．RNA聚合酶 D．解旋酶     

线粒体DNA与DNA甲基化的关系

线粒体DNA（mitochondrial DNA,mtDNA）遗传信息量虽小,却控制着线粒体一些最基本的性质,对细胞及其功能有着重要影响。mtDNA的损伤与衰老、肿瘤等疾病的发生有关。DNA甲基化是调节基因表达的重要方式之一。mtDNA基因的表达受核DNA（nuclear DNA,nDNA）的调控,mtDNA和nDNA协同作用参与机体代谢调节和发病。本文就近年来mtDNA与DNA甲基化的关系作一综述。     

DNA标记的种类、特点及其研究进展

生命的遗传信息存储于DNA序列之中,基因组DNA序列的变异是物种遗传多样性的基础。目前已发展出的DNA标记技术不下十几种,它们各具特色,并被广泛地应用于作物遗传育种、基因定位、亲缘关系鉴别、基因克隆研究等方面。对DNA标记技术进行分类,并作了初步概述。     

Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines

Dominant phenotype of a genetic marker provides incomplete information about the marker genotype of an individual. A consequence of using this incomplete information for mapping quantitative trait loci (QTL) is that the inference of the genotype of a putative QTL flanked by a marker with dominant phenotype will depend on the genotype or phenotype of the next marker. This dependence can be extended further until a marker genotype is fully observed. A general algorithm is derived to calculate the probability distribution of the genotype of a putative QTL at a given genomic position, conditional on all observed marker phenotypes in the region with dominant and missing marker information for an individual. The algorithm is implemented for various populations stemming from two inbred lines in the context of mapping QTL. Simulation results show that if only a proportion of markers contain missing or dominant phenotypes, QTL mapping can be almost as efficient as if there were no missing information in the data. The efficiency of the analysis, however, may decrease substantially when a very large proportion of markers contain missing or dominant phenotypes and a genetic map has to be reconstructed first on the same data as well. So it is important to combine dominant markers with codominant markers in a QTL mapping study. This revised version was published online in July 2006 with corrections to the Cover Date.     

Bayesian analysis of linkage between genetic markers and quantitative trait loci. II. Combining prior knowledge with experimental evidence

Summary A Bayesian method was developed for identifying genetic markers linked to quantitative trait loci (QTL) by analyzing data from daughter or granddaughter designs and single markers or marker pairs. Traditional methods may yield unrealistic results because linkage tests depend on number of markers and QTL gene effects associated with selected markers are overestimated. The Bayesian or posterior probability of linkage combines information from a daughter or granddaughter design with the prior probability of linkage between a marker locus and a QTL. If the posterior probability exceeds a certain quantity, linkage is declared. Upon linkage acceptance, Bayesian estimates of marker-QTL recombination rate and QTL gene effects and frequencies are obtained. The Bayesian estimates of QTL gene effects account for different amounts of information by shrinking information from data toward the mean or mode of a prior exponential distribution of gene effects. Computation of the Bayesian analysis is feasible. Exact results are given for biallelic QTL, and extensions to multiallelic QTL are suggested.     

Genetic diversity and population structure detection in sponge gourd ( Luffa cylindrica ) using ISSR,SCoT and morphological markers

Investigation of genetic diversity is essential for the selection of parents for crop breeding and conservation of genetic resources. To estimate the genetic variability and population structure in the midst of 45 accessions of sponge gourd brought together from different geographical areas of India, morphological traits and two molecular markers, ISSR and SCoT markers were compared. Principal components analysis of 20 morphological traits showed 72.70% variability and significant positive correlations between fruit traits. All three marker techniques clustered all accessions into two groups with few outgroups. High level of polymorphism was observed among ISSR (74.6%) and SCoT (71.5%) primers. The Bayesian model revealed the hidden grouping and showed admixture type of population. The diversity pattern is influenced by genetic marker used, as different molecular markers have different polymorphism evaluation efficiency. This study can be helpful in amplifying the genetic base and selection of specific traits for breeding. Thus, ISSR and SCoT markers are potential marker for identification in sponge gourd and provide valuable data on its genetic correlation and structure.     

Detecting DNA polymorphism and genetic diversity in Lentil (Lens culinaris Medik.) germplasm: comparison of ISSR and DAMD marker

Genetic diversity and interrelationships among 31 lentil genotypes were evaluated using 10 Inter-Simple Sequence Repeat (ISSR) and 10 directed amplification of minisatellite DNA region (DAMD) primers. A total of 43 and 48 polymorphic bands were amplified by ISSR and DAMD markers, respectively. Average polymorphism information content (PIC) for ISSR and DAMD markers were 0.37 and 0.41, respectively. All 31 lentil genotypes could be distinguished by ISSR markers into three groups and by DAMD markers into two groups. Various molecular markers show a different efficiency for evaluating DNA polymorphism in lentil and indicate that the patterns of variation are clearly influenced by the genetic marker used. Comparatively, the genetic diversity of examined lentil genotypes by two different marker techniques (ISSR and DAMD) was high and indicated that ISSR and DAMD are effective and promising marker systems for fingerprinting in lentil and give useful information on its genetic relationships.     

Modeling population genetic data in autotetraploid species

Allozyme and PCR-based molecular markers have been widely used to investigate genetic diversity and population genetic structure in autotetraploid species. However, an empirical but inaccurate approach was often used to infer marker genotype from the pattern and intensity of gel bands. Obviously, this introduces serious errors in prediction of the marker genotypes and severely biases the data analysis. This article developed a theoretical model to characterize genetic segregation of alleles at genetic marker loci in autotetraploid populations and a novel likelihood-based method to estimate the model parameters. The model properly accounts for segregation complexities due to multiple alleles and double reduction at autotetrasomic loci in natural populations, and the method takes appropriate account of incomplete marker phenotype information with respect to genotype due to multiple-dosage allele segregation at marker loci in tetraploids. The theoretical analyses were validated by making use of a computer simulation study and their utility is demonstrated by analyzing microsatellite marker data collected from two populations of sycamore maple (Acer pseudoplatanus L.), an economically important autotetraploid tree species. Numerical analyses based on simulation data indicate that the model parameters can be adequately estimated and double reduction is detected with good power using reasonable sample size.     

Microsatellite marker based genetic diversity analysis among cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>) accessions differing for their response to drought stress

Genetic diversity is an essential input for any plant breeding programme. To assess the genetic divergence among the newly identified drought tolerant lines and elite cotton genotypes including popular varieties, a total of 51 distinctly polymorphic markers were identified after screening 142 genome-wide SSR markers. The identified polymorphic markers detected a total of 140 alleles with a mean of 2.75 alleles per loci and average polymorphism information content of 0.45. Jaccard coefficient based dissimilarity index between the genotypes ranged from 0.18 to 0.82 indicating existence of wide variation between and within the drought tolerant and susceptible genotypes at the DNA level. Cluster and factorial analyses have provided the structure of genetic diversity present and clearly distinguished the drought tolerant and susceptible cotton genotypes. Clustering pattern was in congruence with the source or pedigree of genotypes. The information generated in the present study on genetic divergence among genotypes having differential response to drought will help in selection of suitable lines as parents for developing drought tolerant cultivars in cotton. The polymorphic markers and diverse lines identified in the study will be of immense utility in molecular mapping and marker assisted breeding to achieve drought tolerance in cotton.     

SNP markers: methods of analysis, ways of development, and comparison on an example of common wheat

SNPs (single nucleotide polymorphisms), which belong to the last-generation molecular markers, occur at high frequencies in both animal and plant genomes. The development of SNP markers allows to automatize and enhance tenfolds the effectiveness of genotype analysis. This review summarizes literature data on methods of SNP polymorphism analysis. Various methods of developing SNP markers are considered, taking common wheat Triticum aestivum L. as an example. These markers are compared to other DNA markers, in order to ensure adequate choice of marker type for solving various molecular genetic problems.     

Statistical recovering of incomplete genotypic information of DNA molecular markers

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SNP markers: Methods of analysis, ways of development, and comparison on an example of common wheat

SNPs (single nucleotide polymorphisms), which belong to the last-generation molecular markers, occur at high frequencies in both animal and plant genomes. The development of SNP markers allows to automatize and enhance tenfolds the effectiveness of genotype analysis. This review summarizes literature data on methods of SNP polymorphism analysis. Various methods of developing SNP markers are considered, taking common wheat Triticum aestivum L. as an example. These markers are compared to other DNA markers, in order to ensure adequate choice of marker type for solving various molecular genetic problems.     

Molecular mechanism of genetic recombination in bacterial transformation

Summary B. subtilis cells auxotrophic for two linked markers (ind-his, ind-tyr, his-tyr) have been transformed by means of DNA preparations obtained by hybridization of wild type DNA with the DNA of a strain auxotrophic for one of the linked markers. It was established that hybridization does not increase the transforming activity of DNA for the heterozygous marker. A genetic analysis of the progeny of cells transformed by hybrid or wild type DNA was performed. On the basis of the data obtained a model of genetic recombination in transformation is proved. According to this model both strands of the donor DNA interact independently with the chromosome, and either strand can be incorporated into the cell genome with equal probability. According to the estimate made on the basis of this hypothesis, the probability of integration of a single DNA strand carrying a particular genetic marker is 8%.With 3 Figures in the Text